AMBER Archive (2007)

Subject: Re: AMBER: torsional restraints in a solvated MD simulation.

From: Tom Pochapsky (pochapsk_at_brandeis.edu)
Date: Tue Aug 14 2007 - 20:04:24 CDT

Thanks, Dave & Carlos, your suggestions seemed to work. I am getting
energies for the torsion.

Tom

Tom Pochapsky wrote:
> David A. Case wrote:
>> On Tue, Aug 14, 2007, Tom Pochapsky wrote:
>>
>>> I am trying to force a cis -> trans isomerization of a peptide bond
>>> during a standard solvated MD simulation using Amber 8. I have
>>> included a standard torsion restraint file to be applied
>>> gradually during the simulation, but cannot detect any change;
>>> furthermore, no torsional energies are reported in md.out ,
>>
>> Set pencut to a negative number, if you want to be sure the potential
>> is being
>> applied.
>>
>>>> &rst iat = 1321, 1336, 1338, 1348,
>>>> r1 = -531.0, r2 = -530.0, r3 = -180.0, r4 = -179.0,
>>>> rk2 = 100.0, rk3 = 100.0, &end
>>
>> This is certainly a weird constraint! Because dihedral angles are
>> circular,
>> Amber adds or subtracts 360 degrees from the current angle to get it
>> as close
>> as possible to the center of the flat region, then applies the restraint.
>>
> Oops. I generated this from a five-column DYANA type restraint file,
> but it is possible that since I specified -185 degrees, and the lower
> limit to be -175, this happened. I will try your suggestion and let you
> know how it works.
>
> Thanks, Tom
>
>> In your case, an initial "cis" angle near 0 degrees would be converted
>> to -360
>> degrees (close the midpoint between -530 and -180). The program would
>> then
>> decide that no penalty should be applied (since the current angle is
>> between
>> r2 and r3).
>>
>> Why not set r2 to 170 and r3 to 190 if you want to force the angle to
>> become
>> trans? I'd also suggest lowering rk2 and rk3, but you may want to
>> experiment
>> with that.
>>
>> ....dac
>>
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